One site I just updated – the “Other Miscellaneous Options” button was missing from the plugin admin page.
I’m certain this is a theme CSS conflict – Theme is Mystique 3.2.1.
Anyway, the solution for this is to change the “margin-top:40px;”<center><input class="button-primary" type="submit" name="Save" style="padding-left:40px;padding-right:40px;margin-top:40px;" value="<?php _e('Update Miscellaneous Options','jwl-ultimate-tinymce'); ?>" id="submitbutton" /></center>
(Line 901 in main.php) to a smaller value (I used 4px)
Which moves the button up enough to save the settings.

I’m only posting this so anyone else finding this button missing after an update will know where to look.
(I like the Mystique theme – but it does have a lot of quircks!)